We develop and apply computational genomics approaches to best characterized biological processes in order to reveal novel functional features that cannot be obtained by experimental techniques alone. In this work, we use an array of bioinformatics tools - from sensitive similarity searches to phylogenetics and structure prediction - and several tiers of hardware - from workstations and stand-alone servers to Linux clusters and supercomputers sifting through trillions of letters of DNA and protein sequences in search of answers to basic biological questions.

We are interested in fundamental biological questions, such as signal transduction, gene regulation and protein-protein interactions, which we study through the prism of molecular evolution. Our main focus is on prokaryotes, not only because they display an extraordinary diversity and unexpected complexity, but also because prokaryotic genomes are best suited for in-depth computational analyses using evolutionary genomics. Our credo is simple: Nature has already performed millions of genetic experiments; all we need to do is to carefully analyze the results. Most of our studies generate testable hypotheses that are often taken directly into experiment by our colleagues in "wet" laboratories.

More information, see lab page.

UTK-ORNL Joint Institute for Computational Sciences

• Wisniewski-Dye, F., Borziak, K., Khalsa-Moyers, G., Alexandre, G., Sukharnikov, L.O., Wuichet, K., Hurst, G.B., McDonald, W.H., Robertson, J.S., Barbe, V., Calteau, A., Rouy, Z., Mangenot, S., Prigent-Combaret, C., Normand, P., Boyer, M., Siguier, P., Dessaux, Y., Elmerich, C., Condemine, G., Krishnen, G., Kennedy, I., Paterson, A.H., Gonzalez, V., Mavingui, P., Zhulin, I.B. Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genetics 2011, 7: e1002430.
• Sukharnikov, L.O., Cantwell, B.J., Podar, M., Zhulin, I.B. Cellulases: ambiguous, non-homologous enzymes in a genomic perspective. Trends in Biotechnology 2011, 29: 473-479.
• Wuichet, K., Zhulin I.B. Origins and diversification of a complex signal transduction system in prokaryotes. Science Signaling 2010, 3: ra50
• Wuichet, K., Cantwell, B.J., Zhulin, I.B. Evolution and phyletic distribution of two-component signal transduction systems. Current Opinion in Microbiology 2010, 13: 219-225.
• Xie, Z., Ulrich, L.E., Zhulin, I.B., Alexandre, G. PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis. Proceedings of the National Academy of Sciences of the USA 2010, 107: 2235-2240.
• Ulrich, L.E, Zhulin, I.B. MIST2: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Research 2010, 38: D401-D407. openAccess
• Briegel A, Ortega DR, Tocheva EI, Wuichet K, Li Z, Chen S, Muller A, Iancu CV, Murphy GE, Dobro MJ, Zhulin IB, Jensen GJ. Universal architecture of bacterial chemoreceptor arrays. Proceedings of the National Academy of Sciences of the USA 2009, 106: 17181-17186. Press release.

Pubmed Link

B.S., 1983, Saratov State University, Russia

Ph.D., 1988, St. Petersburg State University, Russia

Postdoctoral Fellow, 1988-1991, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences

Postdoctoral Fellow, 1990-1991, The University of Oxford, United Kingdom

Postdoctoral Fellow, 1992-1996, Loma Linda University School of Medicine, California